High Polymorphism Research Articles

The current state of the problem of diagnosis and therapy of depressive disorders (a literature review)

The article presents the results of an analytical review of current literature data on the problem of diagnosis and treatment of depressive disorders. The issues of a high incidence and polymorphism of the clinical presentation of these disorders are considered. The tendency towards formalization and objectification in the process of diagnosing depressive disorders in modern psychiatric discourse is covered, in particular, through the use of neuroimaging, neurophysiological and biochemical methods with the involvement of machine learning and artificial intelligence technologies. The classic method of a structured or semi-structured interview, as a tool for diagnosing clinical depression, currently remains one of the most common, but it has certain limitations and disadvantages, the most significant of which are a considerable degree of the method subjectivity and its dependence on the perception by specialists conducting the diagnosis, that causes low sensitivity and specificity of this method. The significant role of a general practitioner as a key link in the identification and treatment of the described phenomena, which automatically presents to these specialists a number of professional, qualification and personal requirements, such as knowing pathogenesis of depressive disorders, the features of their pharmacotherapy, skills to build compliant relationships with patients, is highlighted apart. The article also emphasizes the lack of information in available sources about measures to assess the risk of depressive episode recurrence, as well as insufficient attention to the methods of neurophysiological examination and their narrow arsenal. Thus, based on the results of the review, it has been found that a promising direction to improve diagnosis and assessment of therapeutic measure effectiveness, as a part of follow-up among patients with depression, in addition to classical psychodiagnostic tools, is the development and implementation of ethological and neurophysiological methods of examination for objectifying evaluation of patients’ condition and elimination of subjective factors associated with specialists’ perception of patients, as well as symptoms of anosognosia or aggravation.

Development and application of SSR markers of Saposhnikovia divaricata based on transcriptome

Transcriptome sequencing was employed to mine the simple sequence repeat(SSR) locus information of Saposhnikovia divaricata and design specific primers, which aimed to provide a basis for the research on the genetic diversity of S. divaricata germplasm resources. The seed purity, 1 000-seed weight, germination rate, and seed vigor were determined. MISA was used to obtain the SSR locus information from 12 606 unigene longer than 1 kb in the transcriptome database. Forty-three pairs of SSR primers designed in Primer 3 were used to analyze the polymorphism of 28 S. divaricata samples of different sources. The results showed that there were differences in the seed purity, 1 000-seed weight, germination rate, vigor, and seed length and width among S. divaricata samples of different sources. Particularly, the germination rate and seed vigor had significant differences, and HB-ZJK1, NMG-CF4, NMG-BT, NMG-HLE1, and NMG-CF2 had significantly higher 1 000-seed weight, germination rate, and seed vigor than the samples of other sources. Among the 86 233 unigene, 12 606(14.62%) unigene contained 15 958 SSR loci, with one SSR locus every 5 009 bp on average. The SSR loci were mainly single nucleotide and dinucleotide repeats, which were dominated by G/C and TC/AG, respectively. All the primers were screened by using 28 S. divaricata sample from different habitats, and the primers corresponding to the amplification products with clear bands and stable polymorphism were obtained. The clustering results of the biological characteristics and genetic diversity of the 28 S. divaricata samples were basically consistent, and the samples of the same origin(HB-AG1, HB-AG2, HB-ZJK1, and HB-ZJK2) generally gathered together and had close genetic relationship. The SSRs in S. divaricata transcriptome has high frequency, rich types, and high polymorphism, which provides candidate molecular markers for the germplasm identification, genetic map construction, and molecular-assisted breeding.

Cross-Species Transferability of Specific SSR Markers from Carex curvula (Cyperaceae) to Other Carex Species

Microsatellites are codominant markers that, due to their high polymorphism, are a common choice for detecting genetic variability in various organisms, including fungi, plants, and animals. However, the process of developing these markers is both costly and time-consuming. As a result, the cross-species amplification has become a more rapid and more affordable alternative in biological studies. The objective of this study was to assess the applicability of 13 SSR markers, originally designed for Carex curvula, in other 14 species belonging to different sections of the genus. All the markers were successfully transferred with a mean of 90.76%, and 100% transferability was reached in two species (C. baldensis and C. rupestris). The lowest transferability was registered in the G165 marker, which did not produce amplification in six species. Together, the microsatellites amplified a total of 183 alleles, ranging from 10 to 19 alleles per locus, with an average of 14.07. The mean number of different alleles ranged from 0.846 to a maximum of 2.077 per locus. No significant departures from the Hardy–Weinberg equilibrium were detected in polymorphic loci. The transferability of the 13 SSR markers proved highly successful in various Carex species, across different clades and sections of the genus.

Forensic parameters and population analysis of 21 autosomal STR loci in the Wuhu Han population from Anhui Province, East China

Background At present, there are no available genetic data on the AGCU EX22 Kit from the Wuhu Han population. Aim This study investigates the applicability of the AGCU EX22 kit, designed for the Chinese population for forensic analysis and population genetics of the Wuhu Han population. Subjects and methods Bloodstains from 1565 unrelated healthy individuals in Wuhu city, Anhui Province, were collected for analysis. The AGCU EX22 kit was used for amplification, and capillary electrophoresis was used to separate the amplification products. Allele frequencies and forensic parameters were determined. The Wuhu Han population was compared to 10 reference populations through genetic distance, a phylogenetic neighbor-joining tree and principal component analysis. Results In total, 281 alleles and 1187 genotypes were observed. No significant deviations from Hardy-Weinberg equilibrium at any locus were found after Bonferroni’s correction. The 21 autosomal short tandem repeat (STR) genetic markers exhibited high informativeness and polymorphism. The cumulative power of discrimination and power of exclusion were 0.999999999999999999999999913380 and 0.999999996752339, respectively. Population comparisons revealed a genetic affinity between Wuhu Han and southern Han populations, except for the Guangdong Han population, which aligned with the traditional geographical division in China. Conclusion The AGCU EX22 Kit, containing 21 STR loci, is suitable for forensic application and population genetics studies in the Wuhu Han population.

Genetic polymorphism analysis and forensic application evaluation of 57 insertion/deletion polymorphisms from Yi ethnic group in Yunnan

Background As a new kind of diallelic genetic marker, insertion/deletion (InDel) polymorphisms have recently been used in forensic science. However, there are relatively few studies on the forensic evaluation of InDel genetic polymorphisms from different populations. Aim The aim of the present work is to assess the genetic polymorphism and forensic applicability of 57 InDels from the Yi ethnic group and explore the genetic background of this group. Subjects and methods A total sample of 122 unrelated individuals of Yi group from the Yunnan province were genotyped by the AGCU indel 60 Kit. Multiplex population genetic analyses on the same 57 InDels were carried out among the Yunnan Yi group and 29 reference populations. Results The average allele frequency of these loci in the Yi ethnic group was 0.485. Heterozygosity, polymorphism information content, and the power of discrimination were 0.477, 0.362, and 0.612, respectively. The combined power of discrimination and the combined power of exclusion reached to 0.99999999999999999669 and 0.999962965, respectively. The results showed that 57 InDels polymorphisms have high genetic polymorphisms in the Yi ethnic group. Conclusions The 57 InDels could be used for forensic individual identification, paternity testing, and intercontinental population discrimination, with the potential for use in biogeographic ancestry inference.

Genetic Relatedness in Elite Cultivars of Moth Bean using Morpho-agronomic and Molecular Markers

Background: Moth bean is a very nutritive and hardy crop, especially for resource poor-arid agriculture. The limited use of cultivars in moth bean breeding resulted into narrow genetic base. This study aimed to diversify the conical genetic base and developimproved cultivars, through molecular (RAPD) and morpho-agronomic characterization of commercially elite moth bean cultivars. Methods: Elite moth bean cultivars (15) were evaluated for 11 morpho-agronomic traits. Eleven RAPD markers were used to amplify genomic DNA and perform molecular characterization.Clustering approach was used for grouping of the cultivars. Result: RAPD markers revealed high polymorphism in 15 elite moth bean cultivars. The polymorphism information content (PIC) values varied within the range of 0.45 to 0.88, with an average of 0.77. The number of alleles at different loci ranged from 4 to 16, with an average of 10 alleles per locus. When employing UPGMA-based cluster analysis, utilizing 11 morpho-agronomic traits, the cultivars were grouped into four clusters. However, when RAPD markers were used, the cultivars were grouped into five clusters. The Jaccard’s similarity coefficient and Manhattan dissimilarity coefficient fell within the ranges of 0.18 to 0.70 and 0.02 to 0.42, respectively. These values signify the degree of genetic variability within the cultivars. Furthermore, a Mantel test was conducted to examine the correlation between agronomic traits and the RAPD-based matrix. The results showed a negative correlation, but it was not statistically significant.The high PIC values and the successful amplification of multiple loci demonstrate the efficacy of RAPD markers in assessing genetic diversity in moth beans. The study revealed enormous genetic variation among cultivars and crosses can be attempted between cultivars of different groups to create better recombinants in moth bean breeding programmes.

Spatiotemporal Expression Characterization of KRTAP6 Family Genes and Its Effect on Wool Traits.

Keratin-related proteins (KAPs) are structural components of wool fibers and are thought to play a key role in regulating the physical and mechanical properties of fibers. Among all KAP genes (KRTAPs), KRTAP6 gene family (KRTAP6-1, KRTAP6-2, KRTAP6-3, KRTAP6-4, and KRTAP6-5) is a very important member with high polymorphism and notable association with some wool traits. In this study, we used real-time fluorescence quantitative PCR (RT-qPCR) and in situ hybridization to investigate spatiotemporal expression of KRTAP6s. The results revealed that KRTAP6 family genes were significantly expressed during anagen compared to other stages (p < 0.05). And it was found the five genes were expressed predominantly in the dermal papillae, inner and outer root sheaths, and showed a distinct spatiotemporal expression pattern. Also, it was found that KRTAP6-1 and KRTAP6-5 mRNA expression was negatively correlated with wool mean fiber diameter (MFD) and mean staple strength (MSS) (p < 0.05). In summary, the KRTAP6 family genes share a similar spatiotemporal expression pattern. And KRTAP6-1 and KRTAP6-5 may regulate the MFD and MSS of Gansu Alpine fine-wool sheep wool by changing the expression.

Forensic efficiency and population genetic construction of Guizhou Gelao minority from Southwest China revealed by a panel of 23 autosomal STR loci.

The first batch of genetic data for 23 autosomal STRs in 490 Geolao individuals from Guizhou was provided.The 23 STR panel can afford high genetic polymorphisms and discrimination power and can be efficiently applied to forensic practice in Guizhou Gelao population.A complex phylogenetic model influenced by ethnic, geographic, and linguistic factors was uncovered.

Development of polymorphic microsatellite markers for distylous-homostylous Primula secundiflora (Primulaceae) using HiSeq sequencing.

Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.

The distribution of allele frequencies of the 15 Short Tandem Repeats loci in Elaziğ population, Türkiye

The DNA within the Human Genome involves loci with high polymorphism such as short tandem repeats (STR). The STR polymorphism analysis is extensively used for numerous purposes such as identification studies in forensic sciences, paternity tests, genome mapping, and population studies. In this study, blood and swab samples were obtained from 200 unrelated healthy individuals living in Elazig province. DNA was amplified via the AmpFlSTR Identifiler PCR Amplification Kit (Applied Biosystems, USA) to analyze the 15 STR loci. Using the ABI PRISM310 Genetic Analyzer capillary electrophoresis, the samples were analyzed and the allelic ladder was used to compare and identify the alleles of the samples, the distribution of the allele frequencies and peak values were examined. For statistical analysis Arlequin v.3.11 and PowerStats v.1.2 were used to assess the data. To determine if the allele frequencies were compatible with the Hardy-Weinberg (HW) equilibrium, the Markov chain and the Fisher's exact test p-value (p&lt;0.05) were examined. It was determined that the D8S1179 (0.00002), D21S11 (0.00593) and vWA (0.04939) loci were not compatible with the HW equilibrium, but the rest of the loci were compatible. For the loci, the combined power of exclusion is 0.9999995, the combined power of discrimination is 0.9999999999998. The probability of matching for the 15 STR loci was calculated to be 1 in 1.364x10ˉ17. The power of discrimination was quite high when all the loci were considered. The results of this study indicate that the populations residing in the Elaziğ province may benefit from paternity testing, forensic identification, and genomic mapping using the data as an appropriate marker.

Genetic polymorphism and clustering of the Plasmodium cynomolgi Duffy binding protein 1 region II of recent macaque isolates from Peninsular Malaysia.

Plasmodium cynomolgi is a simian malaria parasite that has been increasingly infecting humans. It is naturally present in the long-tailed and pig-tailed macaques in Southeast Asia. The P. cynomolgi Duffy binding protein 1 region II [PcDBP1(II)] plays an essential role in the invasion of the parasite into host erythrocytes. This study investigated the genetic polymorphism, natural selection and haplotype clustering of PcDBP1(II) from wild macaque isolates in Peninsular Malaysia. The genomic DNA of 50 P. cynomolgi isolates was extracted from the macaque blood samples. Their PcDBP1(II) gene was amplified using a semi-nested PCR, cloned into a plasmid vector and subsequently sequenced. The polymorphism, natural selection and haplotypes of PcDBP1(II) were analysed using MEGA X and DnaSP ver.6.12.03 programmes. The analyses revealed high genetic polymorphism of PcDBP1(II) (π = 0.026 ± 0.004; Hd = 0.996 ± 0.001), and it was under purifying (negative) selection. A total of 106 haplotypes of PcDBP1(II) were identified. Phylogenetic and haplotype analyses revealed two groups of PcDBP1(II). Amino acid length polymorphism was observed between the groups, which may lead to possible phenotypic difference between them.

Biochemical and molecular profiling of induced high yielding M3 mutant lines of two Trigonella species: Insights into improved yield potential.

Trigonella, commonly known as Fenugreek, is among the most promising medicinal herbs consumed worldwide due its protein rich dietary contributions. This study involved induced mutagenesis on two Trigonella species (Trigonella foenum-graecum var. PEB and Trigonella corniculata var. Pusa kasuri) using caffeine and sodium azide as mutagens, resulting in the identification of nine high-yielding mutant lines in the M3 generation. Molecular characterization using SCoT markers revealed a high polymorphism of 28.3% and 46.7% in PEB and Pusa kasuri, respectively, facilitating the investigation of genetic divergence among the control and mutant lines. Similarity correlation analysis indicated a high similarity between mutant A and mutant C (0.97) and between mutant J and mutant O (0.88), while the lowest similarity was observed between mutant B and mutant F (0.74) and between control and mutant L (0.58). Mutant F and Mutant J displayed the highest seed yield and its attributing traits, and seed protein content in PEB and Pusa kasuri, respectively. Physiological parameters, including chlorophyll content (Mutants A and N) and carotenoids (mutant A and J), exhibited improvements. Assessment of stomatal and seed characteristics using scanning electron microscopy may lead to improved physiological processes and distinction at the interspecific level, respectively. Methanolic extracts of the control and the mutant lines of both species were subjected to GC-MS analysis, revealing 24 major phytocompounds known for their pharmacological activities (antioxidant, anti-inflammatory, anticancer, etc.). Statistical methods such as Pearson correlation heatmap and pairwise scatter plot matrix provided insights into the correlations and linear associations among parameters for both PEB and Pusa kasuri. The strong correlation between iron content and seeds per pod in the mutant lines suggests a promising avenue for further research. Continued research and breeding efforts using these mutants can lead to significant advancements in agriculture and medicine, benefiting farmers, consumers, and industries alike.

How to Predict Binding Specificity and Ligands for New MHC-II Alleles with MixMHC2pred.

MHC-II molecules are key mediators of antigen presentation in vertebrate species and bind to their ligands with high specificity. The very high polymorphism of MHC-II genes within species and the fast-evolving nature of these genes across species has resulted in tens of thousands of different alleles, with hundreds of new alleles being discovered yearly through large sequencing projects in different species. Here we describe how to use MixMHC2pred to predict the binding specificity of any MHC-II allele directly from its amino acid sequence. We then show how both MHC-II ligands and CD4+ T cell epitopes can be predicted in different species with our approach. MixMHC2pred is available at http://mixmhc2pred.gfellerlab.org/ .

Unraveling intragenomic polymorphisms in the high-quality genome of Hypoxylaceae: a comprehensive study of the rDNA cistron

Sequencing ribosomal DNA loci, such as ITS and LSU, are among the first steps to characterize and identify newly isolated fungal strains. Substantial doubt has recently been raised concerning the unequivocal suitability of using this sequence information for inferring inter- and intraspecific relationships, as especially the ITS locus was repeatedly shown to harbor high intragenomic plasticity. The evolutionary mechanisms leading to this phenomenon are poorly understood, but this is about to change, owing to the availability of third generation sequencing techniques. The current study attempts a comprehensive analysis of rDNA cistrons in the genomes of over 40 selected species of Hypoxylaceae (Xylariales), using a combination of 2nd generation (Illumina) and 3rd generation sequencing technologies (Oxford Nanopore), along with extensive usage of bioinformatic tools to obtain high-quality genomes. Our findings revealed high intragenomic polymorphisms in distinct Hypoxylaceae species, indicating the presence of deep rDNA paralogs. Phylogenetic inference of the ITS rDNA showed low support for the primary clades within Hypoxylaceae, while inference using the protein encoding gene RPB2 showed better support. We also found that proteinogenic genes are not prone to intraspecific and intragenomic polymorphisms as much as the rDNA loci. Our study highlights the limitations of solely relying on the rDNA cistron as a barcode for fungi. We propose TUB2 as a new primary barcoding marker for Hypoxylaceae and other Xylariales. Moreover, we demonstrate the feasibility to retrieve some DNA loci that had hitherto not been used for classical phylogenetic studies (such as TEF1) in Xylariales directly from genomes without the necessity to work with primers.

Oxidoreductase activity of soybeen seedlings at the early stage of ontogenesis

The results of analysis of specific activity and multiple forms of oxidoreductase class enzymes are presented: antioxidant complex (catalase and peroxidase) and dehydrogenases (alcohol dehydrogenase, NAD+-malate dehydrogenase, glucose-6-phosphate dehydrogenase). Seven varieties of soybean (Glycine max (L.) Merrill) served as the object of the study. Dormant seeds and 3- and 7-day-old soybean seedlings were used for the analysis. Protein content was determined by the Lowry method, peroxidase activity was determined by colorimetric, catalase and the studied dehydrogenases – by spectrophotometric methods, electrophoretic spectra of enzymes – by electrophoresis on 7.5% polyacrylamide gel columns. Identification of the zones with enzymatic activity on the gel was performed by appropriate histochemical methods. Analysis of specific activity of antioxidant enzymes in dormant soybean seeds revealed increased activity of peroxidase and low activity of catalase. During seed germination, the inverse relationship of the specific activity of these enzymes is observed. On the 7th day the specific activity of catalase increases, that of peroxidase decreases to a minimum. In soybean germination, 5 forms of catalase were detected, indicating low polymorphism and stability of the enzyme, and 18 forms of peroxidase, which confirm high polymorphism and the possibility of using this enzyme as a marker of biochemical processes. Alcohol dehydrogenase and glucose-6-phosphate dehydrogenase were found to be of low heterogeneity, with the specific activity of these enzymes decreasing during germination compared to the dormant period of soybean seeds. The specific activity of NAD+-malate dehydrogenase increases slightly during germination. Eight forms of this enzyme were detected in the soybean varieties studied indicating increased polymorphism. In dormant soybean seeds, the electrophoretic spectra of NAD+-malate dehydrogenase exhibited varietal diversity allowing the enzyme to be used as a marker for further studies.

Investigation of the variability of chloroplast DNA of some Astragalus spp. of sect. Helmia and A. arcanus of sect. Erioceras (Fabaceae)

Analysis of chloroplast DNA sequences revealed a high polymorphism of the length and nucleotide composition of trnF–trnV and the intron trnL for Helmia section species of the genus Astragalus (Fabaceae). Molecular genetic studies of Astragalus species of the Helmia section were previously practically not carried out; sequencing of trnF–trnV and the intron trnL of chloroplast DNA for 7 species of the section, as well as the probable intersection hybrid Astragalus arcanus held for the first time. On the basis of genetic studies, clarified the relationship between species included in the section Helmia. The possible stages of sect. Helmia evolution are discussed. The taxonomic isolation of Astragalus permiensis has been confirmed; it is assumed not to be of Uralic, but of Siberian or Central Asian origin. Astragalus ionae belongs to the section Helmia is confirmed. Astragalus depauperatus s. l. is thought to be a complex of twin species. In this article, one of them is considered in the status of the species A. chakassiensis. &#x0D; Copy Translate

Genetic diversity analysis of indigenous pomegranate (Punica granatum L.) germplasm lines

Pomegranate (Punica granatum L.) is an ancient edible fruit crop well recognized for its immense nutraceutical and medicinal properties. Precise morphological characterization of wild, exotic and commercial (cultivar) varieties and understanding the molecular variability in perennial crops like pomegranate is essential for developing varietal DNA fingerprints, identifying true-to-type of genotypes, to avoid duplication and overcome the problem of clonal admixture. It has become a challenge to identify varieties based solely on observable phenotypic traits due to dynamic environmental factors that influence physical traits and increasing number of varieties. Hence, the implementation of stable molecular markers is the best complementary biotechnological tool, which fulfil the above requirements. In our first objective, we identified 24 polymorphic SSR markers out of 40. These SSRs screened on 13 different varieties of pomegranate. The PIC value ranged from 0.13 to 0.37 (mean 0.25) and heterozygosity percent ranged from 0.14% to 0.50% (mean 0.35%). Highest PIC value and heterozygosity observed in PgSSR78 marker. Similarity coefficient matrix showed the genetic distance between the twenty-four varieties, ranged from 0.58 to 0.99. Maximum similarity was observed between Alah and Khandari. Minimum similarity was found between IC318743 and 1185 followed by Maha and 1185. PgSSR16, PgSSR23, PgSSR49, PgSSR60, PgSSR32, PgSSR40, PgSSR78 markers were found with high PIC value and heterozygosity and these primers could be useful for pomegranate cultivar identification. From this study, microsatellite markers have proven to be very useful marker for developing varietal identification marker at early growth stage due to its high polymorphism, abundance, multi-allelic and co-dominant inheritance

The Potential of Complementary Sex-Determiner Gene Allelic Diversity for Studying the Number of Patrilines within Honeybee Colonies

Polyandry, a fundamental aspect of honeybee biology, influences genetic diversity within bee colonies. The Csd gene, responsible for sex determination, exhibits a high intraspecific polymorphism, making it a promising candidate for studying patrilines. This study investigates the potential of the complementary sex-determiner gene (Csd) as a marker for genetic studies of honeybee colonies, comparing its efficacy with standard microsatellite markers. A worker bee brood from five colonies was genotyped using both Csd and microsatellite markers. The results showed that Csd alleles offer higher variability than microsatellite markers, providing a superior resolution in genotyping. The number of distinct Csd alleles in each colony surpassed microsatellite markers, demonstrating the potential of Csd for detailed genetic analyses. Despite challenges in Csd amplification efficiency, a two-step nested PCR protocol proved effective. Interestingly, Csd genotyping alone identified more patrilines than the set of five microsatellite markers, emphasizing its efficacy. Combining Csd and microsatellite genotyping enhances the resolution of genetic studies in honeybee colonies, offering valuable insights into genetic diversity, reproductive success, and social dynamics. The Csd gene emerges as a promising tool for advancing genetic studies in honeybee populations.

Development of a Gene-Based Soybean-Origin Discrimination Method Using Allele-Specific Polymerase Chain Reaction.

A low soybean self-sufficiency rate in South Korea has caused a high import dependence and considerable price variation between domestic and foreign soybeans, causing the false labeling of foreign soybeans as domestic. Conventional soybean origin discrimination methods prevent a single-grain analysis and rely on the presence or absence of several compounds or concentration differences. This limits the origin discrimination of mixed samples, demonstrating the need for a method that analyzes individual grains. Therefore, we developed a method for origin discrimination using genetic analysis. The whole-genome sequencing data of the Williams 82 reference cultivar and 15 soybean varieties cultivated in South Korea were analyzed to identify the dense variation blocks (dVBs) with a high single-nucleotide polymorphism density. The PCR primers were prepared and validated for the insertion-deletion (InDel) sequences of the dVBs to discriminate each soybean variety. Our method effectively discriminated domestic and foreign soybean varieties, eliminating their false labeling.

Evaluation of DNA extraction methods for molecular traceability in cold pressed, solvent extracted and refined groundnut oils

Groundnut oil (GNO)/ peanut oil is one of the agro-food products with great economic value and hence an attractive target for adulteration and mislabeling. Simple Sequence Repeats (SSR) are markers of choice for DNA fingerprinting studies as they exhibit high polymorphism due to variable number of repeats. Hence, this study was designed to evaluate and optimized a method for DNA isolation from groundnut oil and study the possibility of using the isolated DNA for molecular traceability using SSR markers. Four methods to isolate DNA from groundnut oil were evaluated. All the four methods were modified CTAB protocols, but differed in procedures forextraction, buffer compositions, amount of oil used and DNA carriers. For molecular traceability of oils, extraction and recovery of DNA from edible oil is a key step, especially in refined oils. A method that employed DNA enrichment prior to extraction with CTAB buffer yielded amplifiable DNA from cold pressed GNO, crude hexaneextracted GNO and refined GNO. The optimized method for isolation of DNA from groundnut oil is simple, efficient, less costly and reproducible when compared to chromatography and spectroscopy based techniques.